[gmx-users] grompp error
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Oct 8 03:40:34 CEST 2011
On 8/10/2011 12:35 AM, Chunxia Gao wrote:
> Dear all,
>
> I generated the molecule topology from antechamber and then coverted to gromcas topology.
>
> When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was no #include "tip3p.itp" . so I added this to the topology file,
> so the topology file looked like this:
>
>
> ; oht.top created by rdparm2gmx.pl Thu Oct 6 22:24:42 IST 2011
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
>
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> c3 c3 0.0000 0.0000 A 3.39967e-01 4.57730e-01
> h1 h1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
> cf cf 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02
> ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> ho ho 0.0000 0.0000 A 0.00000e+00 0.00000e+00
> ce ce 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> os os 0.0000 0.0000 A 3.00001e-01 7.11280e-01
> hc hc 0.0000 0.0000 A 2.64953e-01 6.56888e-02
> oh oh 0.0000 0.0000 A 3.06647e-01 8.80314e-01
> n3 n3 0.0000 0.0000 A 3.25000e-01 7.11280e-01
>
> [ moleculetype ]
> ; Name nrexcl
> solute 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB
> 1 c3 1 OHT C10 1 -0.08830 12.000000
> 2 c3 1 OHT C9 2 -0.04620 12.000000
> 3 ce 1 OHT C8 3 -0.04600 12.000000
> 4 ca 1 OHT C11 4 -0.05100 12.000000
> 5 ca 1 OHT C16 5 -0.11090 12.000000
> 6 ca 1 OHT C15 6 -0.12900 12.000000
> 7 ca 1 OHT C14 7 -0.12960 12.000000
> 8 ca 1 OHT C13 8 -0.13230 12.000000
> 9 ca 1 OHT C12 9 -0.12440 12.000000
> 10 cf 1 OHT C7 10 0.00410 12.000000
> 11 ca 1 OHT C1 11 -0.08660 12.000000
> 12 ca 1 OHT C2 12 -0.07710 12.000000
> 13 ca 1 OHT C3 13 -0.15850 12.000000
> 14 ca 1 OHT C4 14 0.12410 12.000000
> 15 oh 1 OHT O4 15 -0.49780 16.000000
> 16 ca 1 OHT C5 16 -0.21770 12.000000
> 17 ca 1 OHT C6 17 -0.08360 12.000000
> 18 ca 1 OHT C17 18 -0.09110 12.000000
> 19 ca 1 OHT C18 19 -0.08080 12.000000
> 20 ca 1 OHT C19 20 -0.16050 12.000000
> 21 ca 1 OHT C20 21 0.13280 12.000000
> 22 os 1 OHT O20 22 -0.32490 16.000000
> 23 c3 1 OHT C23 23 0.12760 12.000000
> 24 c3 1 OHT C24 24 0.17240 12.000000
> 25 n3 1 OHT N24 25 -0.74670 14.000000
> 26 c3 1 OHT C25 26 0.16000 12.000000
> 27 c3 1 OHT C26 27 0.16650 12.000000
> 28 ca 1 OHT C21 28 -0.20950 12.000000
> 29 ca 1 OHT C22 29 -0.07840 12.000000
> 30 h1 1 OHT H263 30 0.00150 1.000000
> 31 h1 1 OHT H262 31 0.04950 1.000000
> 32 h1 1 OHT H261 32 0.04480 1.000000
> 33 h1 1 OHT H253 33 0.03530 1.000000
> 34 h1 1 OHT H252 34 0.00500 1.000000
> 35 h1 1 OHT H251 35 0.05060 1.000000
> 36 h1 1 OHT H242 36 0.02390 1.000000
> 37 h1 1 OHT H241 37 0.07020 1.000000
> 38 h1 1 OHT H232 38 0.05310 1.000000
> 39 h1 1 OHT H231 39 0.03440 1.000000
> 40 hc 1 OHT H103 40 0.04260 1.000000
> 41 hc 1 OHT H102 41 0.03010 1.000000
> 42 hc 1 OHT H101 42 0.03390 1.000000
> 43 ho 1 OHT HO4 43 0.41810 1.000000
> 44 hc 1 OHT H92 44 0.04990 1.000000
> 45 hc 1 OHT H91 45 0.05550 1.000000
> 46 ha 1 OHT H6 46 0.13840 1.000000
> 47 ha 1 OHT H5 47 0.13260 1.000000
> 48 ha 1 OHT H3 48 0.15160 1.000000
> 49 ha 1 OHT H22 49 0.13540 1.000000
> 50 ha 1 OHT H21 50 0.13480 1.000000
> 51 ha 1 OHT H2 51 0.14400 1.000000
> 52 ha 1 OHT H19 52 0.14860 1.000000
> 53 ha 1 OHT H18 53 0.13890 1.000000
> 54 ha 1 OHT H16 54 0.13590 1.000000
> 55 ha 1 OHT H15 55 0.13110 1.000000
> 56 ha 1 OHT H14 56 0.12990 1.000000
> 57 ha 1 OHT H13 57 0.13140 1.000000
> 58 ha 1 OHT H12 58 0.13240 1.000000
>
> [ bonds ]
> ; ai aj funct r k
> 1 40 1 1.0920e-01 2.8225e+05
> 1 41 1 1.0920e-01 2.8225e+05
> 1 42 1 1.0920e-01 2.8225e+05
> 2 44 1 1.0920e-01 2.8225e+05
> 2 45 1 1.0920e-01 2.8225e+05
> 5 54 1 1.0870e-01 2.8811e+05
> 6 55 1 1.0870e-01 2.8811e+05
> 7 56 1 1.0870e-01 2.8811e+05
> 8 57 1 1.0870e-01 2.8811e+05
> 9 58 1 1.0870e-01 2.8811e+05
> 12 51 1 1.0870e-01 2.8811e+05
> 13 48 1 1.0870e-01 2.8811e+05
> 15 43 1 9.7400e-02 3.0928e+05
> 16 47 1 1.0870e-01 2.8811e+05
> 17 46 1 1.0870e-01 2.8811e+05
> 19 53 1 1.0870e-01 2.8811e+05
> 20 52 1 1.0870e-01 2.8811e+05
> 23 38 1 1.0930e-01 2.8108e+05
> 23 39 1 1.0930e-01 2.8108e+05
> 24 36 1 1.0930e-01 2.8108e+05
> 24 37 1 1.0930e-01 2.8108e+05
> 26 33 1 1.0930e-01 2.8108e+05
> 26 34 1 1.0930e-01 2.8108e+05
> 26 35 1 1.0930e-01 2.8108e+05
> 27 30 1 1.0930e-01 2.8108e+05
> 27 31 1 1.0930e-01 2.8108e+05
> 27 32 1 1.0930e-01 2.8108e+05
> 28 50 1 1.0870e-01 2.8811e+05
> 29 49 1 1.0870e-01 2.8811e+05
> 1 2 1 1.5350e-01 2.5363e+05
> 2 3 1 1.5050e-01 2.7723e+05
> 3 4 1 1.4720e-01 3.0627e+05
> 3 10 1 1.3380e-01 4.7062e+05
> 4 5 1 1.3870e-01 4.0033e+05
> 4 9 1 1.3870e-01 4.0033e+05
> 5 6 1 1.3870e-01 4.0033e+05
> 6 7 1 1.3870e-01 4.0033e+05
> 7 8 1 1.3870e-01 4.0033e+05
> 8 9 1 1.3870e-01 4.0033e+05
> 10 11 1 1.4720e-01 3.0627e+05
> 10 18 1 1.4720e-01 3.0627e+05
> 11 12 1 1.3870e-01 4.0033e+05
> 11 17 1 1.3870e-01 4.0033e+05
> 12 13 1 1.3870e-01 4.0033e+05
> 13 14 1 1.3870e-01 4.0033e+05
> 14 15 1 1.3620e-01 3.2309e+05
> 14 16 1 1.3870e-01 4.0033e+05
> 16 17 1 1.3870e-01 4.0033e+05
> 18 19 1 1.3870e-01 4.0033e+05
> 18 29 1 1.3870e-01 4.0033e+05
> 19 20 1 1.3870e-01 4.0033e+05
> 20 21 1 1.3870e-01 4.0033e+05
> 21 22 1 1.3730e-01 3.1162e+05
> 21 28 1 1.3870e-01 4.0033e+05
> 22 23 1 1.4390e-01 2.5230e+05
> 23 24 1 1.5350e-01 2.5363e+05
> 24 25 1 1.4700e-01 2.6828e+05
> 25 26 1 1.4700e-01 2.6828e+05
> 25 27 1 1.4700e-01 2.6828e+05
> 28 29 1 1.3870e-01 4.0033e+05
>
> [ pairs ]
> ; ai aj funct
> 40 3 1
> 41 3 1
> 42 3 1
> 3 54 1
> 3 58 1
> 4 44 1
> 4 45 1
> 4 55 1
> 4 57 1
> 5 58 1
> 5 56 1
> 6 57 1
> 7 54 1
> 7 58 1
> 8 55 1
> 9 54 1
> 9 56 1
> 10 44 1
> 10 45 1
> 10 51 1
> 10 46 1
> 10 53 1
> 10 49 1
> 11 48 1
> 11 47 1
> 12 46 1
> 13 43 1
> 13 47 1
> 14 51 1
> 14 46 1
> 15 48 1
> 15 47 1
> 16 48 1
> 16 43 1
> 17 51 1
> 18 52 1
> 18 50 1
> 19 49 1
> 20 50 1
> 21 53 1
> 21 38 1
> 21 39 1
> 21 49 1
> 22 52 1
> 22 50 1
> 22 36 1
> 22 37 1
> 24 33 1
> 24 34 1
> 24 35 1
> 24 30 1
> 24 31 1
> 24 32 1
> 25 38 1
> 25 39 1
> 26 36 1
> 26 37 1
> 26 30 1
> 26 31 1
> 26 32 1
> 27 36 1
> 27 37 1
> 27 33 1
> 27 34 1
> 27 35 1
> 28 52 1
> 29 53 1
> 36 38 1
> 36 39 1
> 37 38 1
> 37 39 1
> 40 44 1
> 40 45 1
> 41 44 1
> 41 45 1
> 42 44 1
> 42 45 1
> 46 47 1
> 48 51 1
> 49 50 1
> 52 53 1
> 54 55 1
> 55 56 1
> 56 57 1
> 57 58 1
> 1 4 1
> 1 10 1
> 2 5 1
> 2 9 1
> 2 11 1
> 2 18 1
> 3 6 1
> 3 8 1
> 3 12 1
> 3 17 1
> 3 19 1
> 3 29 1
> 4 11 1
> 4 18 1
> 4 7 1
> 5 10 1
> 5 8 1
> 6 9 1
> 9 10 1
> 10 13 1
> 10 16 1
> 10 20 1
> 10 28 1
> 11 19 1
> 11 29 1
> 11 14 1
> 12 18 1
> 12 16 1
> 12 15 1
> 13 17 1
> 15 17 1
> 17 18 1
> 18 21 1
> 19 28 1
> 19 22 1
> 20 29 1
> 20 23 1
> 21 24 1
> 22 29 1
> 22 25 1
> 23 28 1
> 23 26 1
> 23 27 1
>
> [ angles ]
> ; ai aj ak funct theta cth
> 1 2 44 1 1.1005e+02 3.8802e+02
> 1 2 45 1 1.1005e+02 3.8802e+02
> 2 1 40 1 1.1005e+02 3.8802e+02
> 2 1 41 1 1.1005e+02 3.8802e+02
> 2 1 42 1 1.1005e+02 3.8802e+02
> 3 2 44 1 1.1098e+02 3.9330e+02
> 3 2 45 1 1.1098e+02 3.9330e+02
> 4 5 54 1 1.2001e+02 4.0551e+02
> 4 9 58 1 1.2001e+02 4.0551e+02
> 5 6 55 1 1.2001e+02 4.0551e+02
> 6 5 54 1 1.2001e+02 4.0551e+02
> 6 7 56 1 1.2001e+02 4.0551e+02
> 7 6 55 1 1.2001e+02 4.0551e+02
> 7 8 57 1 1.2001e+02 4.0551e+02
> 8 7 56 1 1.2001e+02 4.0551e+02
> 8 9 58 1 1.2001e+02 4.0551e+02
> 9 8 57 1 1.2001e+02 4.0551e+02
> 11 12 51 1 1.2001e+02 4.0551e+02
> 11 17 46 1 1.2001e+02 4.0551e+02
> 12 13 48 1 1.2001e+02 4.0551e+02
> 13 12 51 1 1.2001e+02 4.0551e+02
> 14 13 48 1 1.2001e+02 4.0551e+02
> 14 15 43 1 1.0947e+02 4.0878e+02
> 14 16 47 1 1.2001e+02 4.0551e+02
> 16 17 46 1 1.2001e+02 4.0551e+02
> 17 16 47 1 1.2001e+02 4.0551e+02
> 18 19 53 1 1.2001e+02 4.0551e+02
> 18 29 49 1 1.2001e+02 4.0551e+02
> 19 20 52 1 1.2001e+02 4.0551e+02
> 20 19 53 1 1.2001e+02 4.0551e+02
> 21 20 52 1 1.2001e+02 4.0551e+02
> 21 28 50 1 1.2001e+02 4.0551e+02
> 22 23 38 1 1.0882e+02 4.2543e+02
> 22 23 39 1 1.0882e+02 4.2543e+02
> 23 24 36 1 1.1007e+02 3.8794e+02
> 23 24 37 1 1.1007e+02 3.8794e+02
> 24 23 38 1 1.1007e+02 3.8794e+02
> 24 23 39 1 1.1007e+02 3.8794e+02
> 25 24 36 1 1.0992e+02 4.1330e+02
> 25 24 37 1 1.0992e+02 4.1330e+02
> 25 26 33 1 1.0992e+02 4.1330e+02
> 25 26 34 1 1.0992e+02 4.1330e+02
> 25 26 35 1 1.0992e+02 4.1330e+02
> 25 27 30 1 1.0992e+02 4.1330e+02
> 25 27 31 1 1.0992e+02 4.1330e+02
> 25 27 32 1 1.0992e+02 4.1330e+02
> 28 29 49 1 1.2001e+02 4.0551e+02
> 29 28 50 1 1.2001e+02 4.0551e+02
> 30 27 31 1 1.0955e+02 3.2786e+02
> 30 27 32 1 1.0955e+02 3.2786e+02
> 31 27 32 1 1.0955e+02 3.2786e+02
> 33 26 34 1 1.0955e+02 3.2786e+02
> 33 26 35 1 1.0955e+02 3.2786e+02
> 34 26 35 1 1.0955e+02 3.2786e+02
> 36 24 37 1 1.0955e+02 3.2786e+02
> 38 23 39 1 1.0955e+02 3.2786e+02
> 40 1 41 1 1.0835e+02 3.2995e+02
> 40 1 42 1 1.0835e+02 3.2995e+02
> 41 1 42 1 1.0835e+02 3.2995e+02
> 44 2 45 1 1.0835e+02 3.2995e+02
> 1 2 3 1 1.1096e+02 5.3304e+02
> 2 3 4 1 1.1911e+02 5.2559e+02
> 2 3 10 1 1.1740e+02 5.4978e+02
> 3 4 5 1 1.2066e+02 5.4292e+02
> 3 4 9 1 1.2066e+02 5.4292e+02
> 3 10 11 1 1.2308e+02 5.4559e+02
> 3 10 18 1 1.2308e+02 5.4559e+02
> 4 3 10 1 1.2308e+02 5.4559e+02
> 4 5 6 1 1.1997e+02 5.6216e+02
> 4 9 8 1 1.1997e+02 5.6216e+02
> 5 4 9 1 1.1997e+02 5.6216e+02
> 5 6 7 1 1.1997e+02 5.6216e+02
> 6 7 8 1 1.1997e+02 5.6216e+02
> 7 8 9 1 1.1997e+02 5.6216e+02
> 10 11 12 1 1.2066e+02 5.4292e+02
> 10 11 17 1 1.2066e+02 5.4292e+02
> 10 18 19 1 1.2066e+02 5.4292e+02
> 10 18 29 1 1.2066e+02 5.4292e+02
> 11 10 18 1 1.1553e+02 5.3974e+02
> 11 12 13 1 1.1997e+02 5.6216e+02
> 11 17 16 1 1.1997e+02 5.6216e+02
> 12 11 17 1 1.1997e+02 5.6216e+02
> 12 13 14 1 1.1997e+02 5.6216e+02
> 13 14 15 1 1.1994e+02 5.8450e+02
> 13 14 16 1 1.1997e+02 5.6216e+02
> 14 16 17 1 1.1997e+02 5.6216e+02
> 15 14 16 1 1.1994e+02 5.8450e+02
> 18 19 20 1 1.1997e+02 5.6216e+02
> 18 29 28 1 1.1997e+02 5.6216e+02
> 19 18 29 1 1.1997e+02 5.6216e+02
> 19 20 21 1 1.1997e+02 5.6216e+02
> 20 21 22 1 1.1920e+02 5.8400e+02
> 20 21 28 1 1.1997e+02 5.6216e+02
> 21 22 23 1 1.1797e+02 5.2108e+02
> 21 28 29 1 1.1997e+02 5.6216e+02
> 22 21 28 1 1.1920e+02 5.8400e+02
> 22 23 24 1 1.0842e+02 5.6718e+02
> 23 24 25 1 1.1038e+02 5.5379e+02
> 24 25 26 1 1.1090e+02 5.3564e+02
> 24 25 27 1 1.1090e+02 5.3564e+02
> 26 25 27 1 1.1090e+02 5.3564e+02
>
> [ dihedrals ]
> ;i j k l func C0 ... C5
> 40 1 2 3 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 41 1 2 3 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 42 1 2 3 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 3 4 5 54 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 3 4 9 58 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 4 3 2 44 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 4 3 2 45 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 4 5 6 55 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 4 9 8 57 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 5 4 9 58 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 5 6 7 56 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 6 7 8 57 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 7 6 5 54 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 7 8 9 58 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 8 7 6 55 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 9 4 5 54 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 9 8 7 56 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 3 2 44 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 10 3 2 45 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 10 11 12 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 11 17 46 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 18 19 53 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 18 29 49 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 11 12 13 48 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 11 17 16 47 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 12 11 17 46 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 13 14 15 43 3 7.53120 0.00000 -7.53120 0.00000 0.00000 0.00000 ;
> 13 14 16 47 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 14 13 12 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 14 16 17 46 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 15 14 13 48 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 15 14 16 47 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 16 14 13 48 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 16 14 15 43 3 7.53120 0.00000 -7.53120 0.00000 0.00000 0.00000 ;
> 17 11 12 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 18 19 20 52 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 18 29 28 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 19 18 29 49 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 20 21 28 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 21 20 19 53 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 21 22 23 38 3 1.60247 4.80742 0.00000 -6.40989 0.00000 0.00000 ;
> 21 22 23 39 3 1.60247 4.80742 0.00000 -6.40989 0.00000 0.00000 ;
> 21 28 29 49 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 22 21 20 52 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 22 21 28 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 22 23 24 36 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ;
> 22 23 24 37 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ;
> 24 25 26 33 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 24 25 26 34 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 24 25 26 35 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 24 25 27 30 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 24 25 27 31 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 24 25 27 32 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 25 24 23 38 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 25 24 23 39 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 26 25 24 36 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 26 25 24 37 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 26 25 27 30 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 26 25 27 31 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 26 25 27 32 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 27 25 24 36 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 27 25 24 37 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 27 25 26 33 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 27 25 26 34 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 27 25 26 35 3 1.25520 3.76560 0.00000 -5.02080 0.00000 0.00000 ;
> 28 21 20 52 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 29 18 19 53 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 36 24 23 38 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 36 24 23 39 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 37 24 23 38 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 37 24 23 39 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 40 1 2 44 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 40 1 2 45 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 41 1 2 44 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 41 1 2 45 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 42 1 2 44 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 42 1 2 45 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ;
> 46 17 16 47 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 48 13 12 51 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 49 29 28 50 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 52 20 19 53 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 54 5 6 55 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 55 6 7 56 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 56 7 8 57 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 57 8 9 58 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 4 6 5 54 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 5 7 6 55 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 6 8 7 56 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 7 9 8 57 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 4 8 9 58 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 11 13 12 51 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 12 14 13 48 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 14 17 16 47 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 11 16 17 46 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 18 20 19 53 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 19 21 20 52 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 21 29 28 50 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 18 28 29 49 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 1 2 3 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 1 2 3 10 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ;
> 2 3 4 5 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 2 3 4 9 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 2 3 10 11 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 2 3 10 18 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 3 4 5 6 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 3 4 9 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 3 10 11 12 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 3 10 11 17 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 3 10 18 19 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 3 10 18 29 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 4 3 10 11 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 4 3 10 18 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 4 5 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 4 9 8 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 5 4 3 10 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 5 4 9 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 5 6 7 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 6 5 4 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 6 7 8 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 9 4 3 10 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ;
> 10 11 12 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 11 17 16 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 18 19 20 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 10 18 29 28 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 11 10 18 19 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 11 10 18 29 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 11 12 13 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 11 17 16 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 12 11 10 18 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 12 11 17 16 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 12 13 14 15 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 12 13 14 16 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 13 12 11 17 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 13 14 16 17 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 15 14 16 17 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 17 11 10 18 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ;
> 18 19 20 21 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 18 29 28 21 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 19 18 29 28 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 19 20 21 22 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 19 20 21 28 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 20 19 18 29 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 20 21 22 23 3 7.53120 0.00000 -7.53120 0.00000 0.00000 0.00000 ;
> 20 21 28 29 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 21 22 23 24 3 1.60247 4.80742 0.00000 -6.40989 0.00000 0.00000 ;
> 22 21 28 29 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;
> 22 23 24 25 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;
> 23 22 21 28 3 7.53120 0.00000 -7.53120 0.00000 0.00000 0.00000 ;
> 23 24 25 26 3 5.27184 3.76560 -4.01664 -5.02080 0.00000 0.00000 ;
> 23 24 25 27 3 5.27184 3.76560 -4.01664 -5.02080 0.00000 0.00000 ;
> 2 4 3 10 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 5 9 4 3 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 11 18 10 3 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 12 17 11 10 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 13 16 14 15 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 19 29 18 10 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
> 20 28 21 22 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ;
>
>
> ; water topology
> #include "tip3p.itp"
grompp is not detecting the change of [moleculetype], so you will have
to look at the contents of that tip3p.itp and see why. I think you will
need to #include some standard force field to get the water parameters.
Put the #include for tip3p.itp above your [moleculetype] to get some
different diagnostics that may be more helpful.
Mark
>
> [ system ]
> 58 system in water
>
> [ molecules ]
> ; Compound nmols
> solute 1
> SOL 1339
>
>
> and this time it gave me another wrong message: [ file tip3p.itp, line 52 ]:
> Atom index (1) in settles out of bounds (1-0).
> This probably means that you have inserted topology section "settles"
> in a part belonging to a different molecule than you intended to.
> In that case move the "settles" section to the right molecule.
>
> I cannot figure out why, does anyone have any idea about this?
>
> Regards
> Chunxia
>
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